Currently in the pop-culture zeitgeist, probably Duplikate. A lot of these characters have had their time in terms of hatred though. Back in the day it was scrappy, a couple years ago (for gamers) it might've been D'vorah. But I think anime wise, considering just how large the one piece fandom is, and how evil the world government is, probably Saint Charlos.
I didn't really like Giorno a few years ago, but honestly as the years have gone by I don't think he's anywhere near the worse JoJo character.